moreo
/
QuaPy
1
0
Fork 1
Code Issues Pull Requests Releases Wiki Activity

refactoring aggregative quantifiers

This commit is contained in:
Alejandro Moreo Fernandez 2023-11-12 13:04:19 +01:00
parent 29db15ae25
commit 25f1cc29a3
2 changed files with 119 additions and 41 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
quapy/classification/calibration.py
View File

@ -59,7 +59,7 @@ class RecalibratedProbabilisticClassifierBase(BaseEstimator, RecalibratedProbabi
elif isinstance(k, float): elif isinstance(k, float):
if not (0 < k < 1): if not (0 < k < 1):
raise ValueError('wrong value for val_split: the proportion of validation documents must be in (0,1)') raise ValueError('wrong value for val_split: the proportion of validation documents must be in (0,1)')
return self.fit_cv(X, y) return self.fit_tr_val(X, y)
def fit_cv(self, X, y): def fit_cv(self, X, y):
""" """
@ -94,7 +94,7 @@ class RecalibratedProbabilisticClassifierBase(BaseEstimator, RecalibratedProbabi
self.classifier.fit(Xtr, ytr) self.classifier.fit(Xtr, ytr)
posteriors = self.classifier.predict_proba(Xva) posteriors = self.classifier.predict_proba(Xva)
nclasses = len(np.unique(yva)) nclasses = len(np.unique(yva))
self.calibrator = self.calibrator(posteriors, np.eye(nclasses)[yva], posterior_supplied=True) self.calibration_function = self.calibrator(posteriors, np.eye(nclasses)[yva], posterior_supplied=True)
return self return self
def predict(self, X): def predict(self, X):

156
quapy/method/aggregative.py
View File

@ -1,4 +1,4 @@
from abc import abstractmethod from abc import ABC, abstractmethod
from copy import deepcopy from copy import deepcopy
from typing import Callable, Union from typing import Callable, Union
import numpy as np import numpy as np
@ -19,25 +19,55 @@ from quapy.method.base import BaseQuantifier, BinaryQuantifier, OneVsAllGeneric
# Abstract classes # Abstract classes
# ------------------------------------ # ------------------------------------
class AggregativeQuantifier(BaseQuantifier): class AggregativeQuantifier(ABC, BaseQuantifier):
""" """
Abstract class for quantification methods that base their estimations on the aggregation of classification Abstract class for quantification methods that base their estimations on the aggregation of classification
results. Aggregative Quantifiers thus implement a :meth:`classify` method and maintain a :attr:`classifier` results. Aggregative quantifiers implement a pipeline that consists of generating classification predictions
attribute. Subclasses of this abstract class must implement the method :meth:`aggregate` which computes the and aggregating them. For this reason, the training phase is implemented by :meth:`classification_fit` followed
aggregation of label predictions. The method :meth:`quantify` comes with a default implementation based on by :meth:`aggregation_fit`, while the testing phase is implemented by :meth:`classify` followed by
:meth:`classify` and :meth:`aggregate`. :meth:`aggregate`. Subclasses of this abstract class must provide implementations for these methods.
Aggregative quantifiers also maintain a :attr:`classifier` attribute.
The method :meth:`fit` comes with a default implementation based on :meth:`classification_fit`
and :meth:`aggregation_fit`.
The method :meth:`quantify` comes with a default implementation based on :meth:`classify`
and :meth:`aggregate`.
""" """
@abstractmethod
def fit(self, data: LabelledCollection, fit_classifier=True): def fit(self, data: LabelledCollection, fit_classifier=True):
""" """
Trains the aggregative quantifier Trains the aggregative quantifier. This comes down to training a classifier and an aggregation function.
:param data: a :class:`quapy.data.base.LabelledCollection` consisting of the training data :param data: a :class:`quapy.data.base.LabelledCollection` consisting of the training data
:param fit_classifier: whether or not to train the learner (default is True). Set to False if the :param fit_classifier: whether to train the learner (default is True). Set to False if the
learner has been trained outside the quantifier. learner has been trained outside the quantifier.
:return: self :return: self
""" """
classif_predictions = self.classification_fit(data, fit_classifier)
self.aggregation_fit(classif_predictions)
return self
@abstractmethod
def classification_fit(self, data: LabelledCollection, fit_classifier=True):
"""
Trains the classifier if requested (`fit_classifier=True`) and generate the necessary predictions to
train the aggregation function.
:param data: a :class:`quapy.data.base.LabelledCollection` consisting of the training data
:param fit_classifier: whether to train the learner (default is True). Set to False if the
learner has been trained outside the quantifier.
"""
...
@abstractmethod
def aggregation_fit(self, classif_predictions):
"""
Trains the aggregation function.
:param classif_predictions: typically an `ndarray` containing the label predictions, but could be a
tuple containing any information needed for fitting the aggregation function
"""
... ...
@property @property
@ -101,7 +131,7 @@ class AggregativeQuantifier(BaseQuantifier):
return self.classifier.classes_ return self.classifier.classes_
class AggregativeProbabilisticQuantifier(AggregativeQuantifier): class AggregativeProbabilisticQuantifier(AggregativeQuantifier, ABC):
""" """
Abstract class for quantification methods that base their estimations on the aggregation of posterior probabilities Abstract class for quantification methods that base their estimations on the aggregation of posterior probabilities
as returned by a probabilistic classifier. Aggregative Probabilistic Quantifiers thus extend Aggregative as returned by a probabilistic classifier. Aggregative Probabilistic Quantifiers thus extend Aggregative
@ -227,9 +257,9 @@ class CC(AggregativeQuantifier):
def __init__(self, classifier: BaseEstimator): def __init__(self, classifier: BaseEstimator):
self.classifier = classifier self.classifier = classifier
def fit(self, data: LabelledCollection, fit_classifier=True): def classification_fit(self, data: LabelledCollection, fit_classifier=True):
""" """
Trains the Classify & Count method unless `fit_classifier` is False, in which case, the classifier is assumed to Trains the classifier unless `fit_classifier` is False, in which case, the classifier is assumed to
be already fit and there is nothing else to do. be already fit and there is nothing else to do.
:param data: a :class:`quapy.data.base.LabelledCollection` consisting of the training data :param data: a :class:`quapy.data.base.LabelledCollection` consisting of the training data
@ -237,7 +267,15 @@ class CC(AggregativeQuantifier):
:return: self :return: self
""" """
self.classifier, _ = _training_helper(self.classifier, data, fit_classifier) self.classifier, _ = _training_helper(self.classifier, data, fit_classifier)
return self return None
def aggregation_fit(self, classif_predictions: np.ndarray):
"""
Nothing to do here!
:param classif_predictions: this is actually None
"""
pass
def aggregate(self, classif_predictions: np.ndarray): def aggregate(self, classif_predictions: np.ndarray):
""" """
@ -269,9 +307,10 @@ class ACC(AggregativeQuantifier):
self.val_split = val_split self.val_split = val_split
self.n_jobs = qp._get_njobs(n_jobs) self.n_jobs = qp._get_njobs(n_jobs)
def fit(self, data: LabelledCollection, fit_classifier=True, val_split: Union[float, int, LabelledCollection] = None): def classification_fit(self, data: LabelledCollection, fit_classifier=True, val_split: Union[float, int, LabelledCollection] = None):
""" """
Trains a ACC quantifier. Trains the classifier and generates, optionally through a cross-validation procedure, the predictions
needed for estimating the misclassification rates matrix.
:param data: the training set :param data: the training set
:param fit_classifier: set to False to bypass the training (the learner is assumed to be already fit) :param fit_classifier: set to False to bypass the training (the learner is assumed to be already fit)
@ -281,18 +320,24 @@ class ACC(AggregativeQuantifier):
cross validation to estimate the parameters cross validation to estimate the parameters
:return: self :return: self
""" """
if val_split is None: if val_split is None:
val_split = self.val_split val_split = self.val_split
self.classifier, y, y_, classes, class_count = cross_generate_predictions( self.classifier, true_labels, pred_labels, classes, class_count = cross_generate_predictions(
data, self.classifier, val_split, probabilistic=False, fit_classifier=fit_classifier, n_jobs=self.n_jobs data, self.classifier, val_split, probabilistic=False, fit_classifier=fit_classifier, n_jobs=self.n_jobs
) )
self.cc = CC(self.classifier) return (true_labels, pred_labels)
self.Pte_cond_estim_ = self.getPteCondEstim(self.classifier.classes_, y, y_)
return self def aggregation_fit(self, classif_predictions):
"""
Nothing to do here!
:param classif_predictions: this is actually None
"""
true_labels, pred_labels = classif_predictions
self.cc = CC(self.classifier)
self.Pte_cond_estim_ = self.getPteCondEstim(self.classifier.classes_, true_labels, pred_labels)
@classmethod @classmethod
def getPteCondEstim(cls, classes, y, y_): def getPteCondEstim(cls, classes, y, y_):
@ -348,10 +393,18 @@ class PCC(AggregativeProbabilisticQuantifier):
def __init__(self, classifier: BaseEstimator): def __init__(self, classifier: BaseEstimator):
self.classifier = classifier self.classifier = classifier
def fit(self, data: LabelledCollection, fit_classifier=True): def classification_fit(self, data: LabelledCollection, fit_classifier=True):
self.classifier, _ = _training_helper(self.classifier, data, fit_classifier, ensure_probabilistic=True) self.classifier, _ = _training_helper(self.classifier, data, fit_classifier, ensure_probabilistic=True)
return self return self
def aggregation_fit(self, classif_predictions: np.ndarray):
"""
Nothing to do here!
:param classif_predictions: this is actually None
"""
pass
def aggregate(self, classif_posteriors): def aggregate(self, classif_posteriors):
return F.prevalence_from_probabilities(classif_posteriors, binarize=False) return F.prevalence_from_probabilities(classif_posteriors, binarize=False)
@ -376,30 +429,37 @@ class PACC(AggregativeProbabilisticQuantifier):
self.val_split = val_split self.val_split = val_split
self.n_jobs = qp._get_njobs(n_jobs) self.n_jobs = qp._get_njobs(n_jobs)
def fit(self, data: LabelledCollection, fit_classifier=True, val_split: Union[float, int, LabelledCollection] = None): def classification_fit(self, data: LabelledCollection, fit_classifier=True, val_split: Union[float, int, LabelledCollection] = None):
""" """
Trains a PACC quantifier. Trains the soft classifier and generates, optionally through a cross-validation procedure, the posterior
probabilities needed for estimating the misclassification rates matrix.
:param data: the training set :param data: the training set
:param fit_classifier: set to False to bypass the training (the learner is assumed to be already fit) :param fit_classifier: set to False to bypass the training (the learner is assumed to be already fit)
:param val_split: either a float in (0,1) indicating the proportion of training instances to use for :param val_split: either a float in (0,1) indicating the proportion of training instances to use for
validation (e.g., 0.3 for using 30% of the training set as validation data), or a LabelledCollection validation (e.g., 0.3 for using 30% of the training set as validation data), or a LabelledCollection
indicating the validation set itself, or an int indicating the number k of folds to be used in kFCV indicating the validation set itself, or an int indicating the number `k` of folds to be used in `k`-fold
to estimate the parameters cross validation to estimate the parameters
:return: self :return: self
""" """
if val_split is None: if val_split is None:
val_split = self.val_split val_split = self.val_split
self.classifier, y, y_, classes, class_count = cross_generate_predictions( self.classifier, true_labels, posteriors, classes, class_count = cross_generate_predictions(
data, self.classifier, val_split, probabilistic=True, fit_classifier=fit_classifier, n_jobs=self.n_jobs data, self.classifier, val_split, probabilistic=True, fit_classifier=fit_classifier, n_jobs=self.n_jobs
) )
self.pcc = PCC(self.classifier) return (true_labels, posteriors)
self.Pte_cond_estim_ = self.getPteCondEstim(classes, y, y_)
return self def aggregation_fit(self, classif_predictions):
"""
Nothing to do here!
:param classif_predictions: this is actually None
"""
true_labels, posteriors = classif_predictions
self.pcc = PCC(self.classifier)
self.Pte_cond_estim_ = self.getPteCondEstim(self.classifier.classes_, true_labels, posteriors)
@classmethod @classmethod
def getPteCondEstim(cls, classes, y, y_): def getPteCondEstim(cls, classes, y, y_):
@ -449,7 +509,13 @@ class EMQ(AggregativeProbabilisticQuantifier):
self.exact_train_prev = exact_train_prev self.exact_train_prev = exact_train_prev
self.recalib = recalib self.recalib = recalib
def fit(self, data: LabelledCollection, fit_classifier=True): def classification_fit(self, data: LabelledCollection, fit_classifier=True):
self.classifier, true_labels, posteriors, classes, class_count = cross_generate_predictions(
data, self.classifier, val_split, probabilistic=True, fit_classifier=fit_classifier, n_jobs=self.n_jobs
)
return (true_labels, posteriors)
if self.recalib is not None: if self.recalib is not None:
if self.recalib == 'nbvs': if self.recalib == 'nbvs':
self.classifier = NBVSCalibration(self.non_calibrated) self.classifier = NBVSCalibration(self.non_calibrated)
@ -477,7 +543,15 @@ class EMQ(AggregativeProbabilisticQuantifier):
nfolds=3, nfolds=3,
random_state=0 random_state=0
) )
return self return None
def aggregation_fit(self, classif_predictions: np.ndarray):
"""
Nothing to do here!
:param classif_predictions: this is actually None
"""
pass
def aggregate(self, classif_posteriors, epsilon=EPSILON): def aggregate(self, classif_posteriors, epsilon=EPSILON):
priors, posteriors = self.EM(self.train_prevalence, classif_posteriors, epsilon) priors, posteriors = self.EM(self.train_prevalence, classif_posteriors, epsilon)
@ -768,7 +842,7 @@ class DMy(AggregativeProbabilisticQuantifier):
distributions = np.cumsum(distributions, axis=1) distributions = np.cumsum(distributions, axis=1)
return distributions return distributions
def fit(self, data: LabelledCollection, fit_classifier=True, val_split: Union[float, LabelledCollection] = None): def classification_fit(self, data: LabelledCollection, fit_classifier=True, val_split: Union[float, LabelledCollection] = None):
""" """
Trains the classifier (if requested) and generates the validation distributions out of the training data. Trains the classifier (if requested) and generates the validation distributions out of the training data.
The validation distributions have shape `(n, ch, nbins)`, with `n` the number of classes, `ch` the number of The validation distributions have shape `(n, ch, nbins)`, with `n` the number of classes, `ch` the number of
@ -787,15 +861,19 @@ class DMy(AggregativeProbabilisticQuantifier):
if val_split is None: if val_split is None:
val_split = self.val_split val_split = self.val_split
self.classifier, y, posteriors, classes, class_count = cross_generate_predictions( self.classifier, true_labels, posteriors, classes, class_count = cross_generate_predictions(
data, self.classifier, val_split, probabilistic=True, fit_classifier=fit_classifier, n_jobs=self.n_jobs data, self.classifier, val_split, probabilistic=True, fit_classifier=fit_classifier, n_jobs=self.n_jobs
) )
self.validation_distribution = np.asarray( return (true_labels, posteriors)
[self.__get_distributions(posteriors[y==cat]) for cat in range(data.n_classes)]
)
return self def aggregation_fit(self, classif_predictions):
true_labels, posteriors = classif_predictions
n_classes = len(self.classifier.classes_)
self.validation_distribution = np.asarray(
[self.__get_distributions(posteriors[true_labels == cat]) for cat in range(n_classes)]
)
def aggregate(self, posteriors: np.ndarray): def aggregate(self, posteriors: np.ndarray):
""" """